Using AI, researchers identified one tiny molecular interaction that viruses need to infect cells. Disrupting it stopped the virus before infection could begin.
Washington State University scientists have uncovered a method to interfere with a key viral protein, stopping viruses from getting inside cells where they can cause disease. The discovery points toward a possible new strategy for developing antiviral treatments in the future.
The work, published in the journal Nanoscale, involved researchers from the School of Mechanical and Materials Engineering and the Department of Veterinary Microbiology and Pathology. Together, they identified and disrupted a specific molecular interaction that herpes viruses depend on to enter cells.
"Viruses are very smart," said Jin Liu, corresponding author of the study and a professor in the School of Mechanical and Materials Engineering. "The whole process of invading cells is very complex, and there are a lot of interactions. Not all of the interactions are equally important — most of them may just be background noise, but there are some critical interactions."
Targeting the Protein Viruses Use to Break In
The researchers focused on a viral "fusion" protein, which herpes viruses use to attach to cells and merge with them, triggering infection and disease. Scientists still lack a clear understanding of how this large and complicated protein changes shape to allow viruses inside cells. This limited knowledge is one reason vaccines for many common herpes viruses have remained elusive.
How AI Narrowed Down Thousands of Possibilities
To tackle this challenge, the team turned to artificial intelligence and molecular scale simulations. Professors Prashanta Dutta and Jin Liu analyzed thousands of possible interactions within the fusion protein to find a single amino acid that plays a central role in viral entry. They designed an algorithm to examine interactions among amino acids, the basic building blocks of proteins, and then applied machine learning to sort through the data and identify which interactions mattered most.
A Single Mutation That Blocks Infection
Once the key amino acid was identified, laboratory experiments led by Anthony Nicola from the Department of Veterinary Microbiology and Pathology put the findings to the test. By altering that one amino acid, the researchers found that the virus could no longer successfully fuse with cells. As a result, the herpes virus was effectively prevented from entering the cells.
According to Liu, the computational work was essential because testing even one interaction in the lab can take months. Narrowing the focus ahead of time made the experimental phase far more efficient.
"It was just a single interaction from thousands of interactions. If we don't do the simulation and instead did this work by trial and error, it could have taken years to find," said Liu. "The combination of theoretical computational work with the experiments is so efficient and can accelerate the discovery of these important biological interactions."
What Scientists Still Need to Understand
Although the team confirmed the importance of this specific interaction, many questions remain about how changing one amino acid affects the structure of the entire fusion protein. The researchers plan to continue using simulations and machine learning to better understand how small molecular changes influence the protein at larger scales.
"There is a gap between what the experimentalists see and what we can see in the simulation," said Liu. "The next step is how this small interaction affects the structural change at larger scales. That is also very challenging for us."
Reference: "Modulation of specific interactions within a viral fusion protein predicted from machine learning blocks membrane fusion" by Ryan E. Odstrcil, Albina O. Makio, McKenna A. Hull, Prashanta Dutta, Anthony V. Nicola and Jin Liu, 4 November 2025, Nanoscale.
DOI: 10.1039/D5NR03235K
In addition to Liu, Dutta and Nicola, the project was conducted by PhD students Ryan Odstrcil, Albina Makio, and McKenna Hull. The work was funded by the National Institutes of Health.
News
AI Helped Scientists Stop a Virus With One Tiny Change
Using AI, researchers identified one tiny molecular interaction that viruses need to infect cells. Disrupting it stopped the virus before infection could begin. Washington State University scientists have uncovered a method to interfere with a key [...]
Deadly Hospital Fungus May Finally Have a Weakness
A deadly, drug-resistant hospital fungus may finally have a weakness—and scientists think they’ve found it. Researchers have identified a genetic process that could open the door to new treatments for a dangerous fungal infection [...]
Fever-Proof Bird Flu Variant Could Fuel the Next Pandemic
Bird flu viruses present a significant risk to humans because they can continue replicating at temperatures higher than a typical fever. Fever is one of the body’s main tools for slowing or stopping viral [...]
What could the future of nanoscience look like?
Society has a lot to thank for nanoscience. From improved health monitoring to reducing the size of electronics, scientists’ ability to delve deeper and better understand chemistry at the nanoscale has opened up numerous [...]
Scientists Melt Cancer’s Hidden “Power Hubs” and Stop Tumor Growth
Researchers discovered that in a rare kidney cancer, RNA builds droplet-like hubs that act as growth control centers inside tumor cells. By engineering a molecular switch to dissolve these hubs, they were able to halt cancer [...]
Platelet-inspired nanoparticles could improve treatment of inflammatory diseases
Scientists have developed platelet-inspired nanoparticles that deliver anti-inflammatory drugs directly to brain-computer interface implants, doubling their effectiveness. Scientists have found a way to improve the performance of brain-computer interface (BCI) electrodes by delivering anti-inflammatory drugs directly [...]
After 150 years, a new chapter in cancer therapy is finally beginning
For decades, researchers have been looking for ways to destroy cancer cells in a targeted manner without further weakening the body. But for many patients whose immune system is severely impaired by chemotherapy or radiation, [...]
Older chemical libraries show promise for fighting resistant strains of COVID-19 virus
SARS‑CoV‑2, the virus that causes COVID-19, continues to mutate, with some newer strains becoming less responsive to current antiviral treatments like Paxlovid. Now, University of California San Diego scientists and an international team of [...]
Lower doses of immunotherapy for skin cancer give better results, study suggests
According to a new study, lower doses of approved immunotherapy for malignant melanoma can give better results against tumors, while reducing side effects. This is reported by researchers at Karolinska Institutet in the Journal of the National [...]
Researchers highlight five pathways through which microplastics can harm the brain
Microplastics could be fueling neurodegenerative diseases like Alzheimer's and Parkinson's, with a new study highlighting five ways microplastics can trigger inflammation and damage in the brain. More than 57 million people live with dementia, [...]
Tiny Metal Nanodots Obliterate Cancer Cells While Largely Sparing Healthy Tissue
Scientists have developed tiny metal-oxide particles that push cancer cells past their stress limits while sparing healthy tissue. An international team led by RMIT University has developed tiny particles called nanodots, crafted from a metallic compound, [...]
Gold Nanoclusters Could Supercharge Quantum Computers
Researchers found that gold “super atoms” can behave like the atoms in top-tier quantum systems—only far easier to scale. These tiny clusters can be customized at the molecular level, offering a powerful, tunable foundation [...]
A single shot of HPV vaccine may be enough to fight cervical cancer, study finds
WASHINGTON -- A single HPV vaccination appears just as effective as two doses at preventing the viral infection that causes cervical cancer, researchers reported Wednesday. HPV, or human papillomavirus, is very common and spread [...]
New technique overcomes technological barrier in 3D brain imaging
Scientists at the Swiss Light Source SLS have succeeded in mapping a piece of brain tissue in 3D at unprecedented resolution using X-rays, non-destructively. The breakthrough overcomes a long-standing technological barrier that had limited [...]
Scientists Uncover Hidden Blood Pattern in Long COVID
Researchers found persistent microclot and NET structures in Long COVID blood that may explain long-lasting symptoms. Researchers examining Long COVID have identified a structural connection between circulating microclots and neutrophil extracellular traps (NETs). The [...]
This Cellular Trick Helps Cancer Spread, but Could Also Stop It
Groups of normal cbiells can sense far into their surroundings, helping explain cancer cell migration. Understanding this ability could lead to new ways to limit tumor spread. The tale of the princess and the [...]
